The wording on page 159 of the Inquisitor's Handbook thoroughly confuses me. Table 5-4 seems to list the steep prices for booking passage on a ship.

Then comes weird table 5-5, which lists additional costs for meals and bedding, but if these need to be paid for separately, then what is it exactly that the PCs are paying for in Table 5-4?

The ticket, which allow entrence to the ship and passing to its destination. Which is then modified depending on what quality food and lodgin is offered. In some cases I can imagine that a ship wouldnt provide either food or bed, or that the players in a scrooge moment decide to bring their own food and duffelbags to save some cash.

...or otherwise avoiding check-in and going undercover under the deck plates where the gribblies live...

Bilge Scrapers would call it cozy.